OpenRaiser/Intern-Atlas huggingface dataset:
Towards Robust Partially Supervised Multi-Structure Medical Image Segmentation on Small-Scale Data
Venue: arXiv cs.CV 2021
Year: 2021

The data-driven nature of deep learning (DL) models for semantic segmentation requires a large number of pixel-level annotations. However, large-scale and fully labeled medical datasets are often unavailable for practical tasks. Recently, partially supervised methods have been proposed to utilize images with incomplete labels in the medical domain. To bridge the methodological gaps in partially supervised learning (PSL) under data scarcity, we propose Vicinal Labels Under Uncertainty (VLUU), a simple yet efficient framework utilizing the human structure similarity for partially supervised medical image segmentation. Motivated by multi-task learning and vicinal risk minimization, VLUU transforms the partially supervised problem into a fully supervised problem by generating vicinal labels. We systematically evaluate VLUU under the challenges of small-scale data, dataset shift, and class imbalance on two commonly used segmentation datasets for the tasks of chest organ segmentation and optic disc-and-cup segmentation. The experimental results show that VLUU can consistently outperform previous partially supervised models in these settings. Our research suggests a new research direction in label-efficient deep learning with partial supervision.
FaceGuard: A Self-Supervised Defense Against Adversarial Face Images
Venue: arXiv cs.CV 2021
Year: 2021

Prevailing defense mechanisms against adversarial face images tend to overfit to the adversarial perturbations in the training set and fail to generalize to unseen adversarial attacks. We propose a new self-supervised adversarial defense framework, namely FaceGuard, that can automatically detect, localize, and purify a wide variety of adversarial faces without utilizing pre-computed adversarial training samples. During training, FaceGuard automatically synthesizes challenging and diverse adversarial attacks, enabling a classifier to learn to distinguish them from real faces and a purifier attempts to remove the adversarial perturbations in the image space. Experimental results on LFW dataset show that FaceGuard can achieve 99.81% detection accuracy on six unseen adversarial attack types. In addition, the proposed method can enhance the face recognition performance of ArcFace from 34.27% TAR @ 0.1% FAR under no defense to 77.46% TAR @ 0.1% FAR.
A method for large diffeomorphic registration via broken geodesics
Venue: arXiv cs.CV 2021
Year: 2021

Anatomical variabilities seen in longitudinal data or inter-subject data is usually described by the underlying deformation, captured by non-rigid registration of these images. Stationary Velocity Field (SVF) based non-rigid registration algorithms are widely used for registration. SVF based methods form a metric-free framework which captures a finite dimensional submanifold of deformations embedded in the infinite dimensional smooth manifold of diffeomorphisms. However, these methods cover only a limited degree of deformations. In this paper, we address this limitation and define an approximate metric space for the manifold of diffeomorphisms $\mathcal{G}$. We propose a method to break down the large deformation into finite compositions of small deformations. This results in a broken geodesic path on $\mathcal{G}$ and its length now forms an approximate registration metric. We illustrate the method using a simple, intensity-based, log-demon implementation. Validation results of the proposed method show that it can capture large and complex deformations while producing qualitatively better results than the state-of-the-art methods. The results also demonstrate that the proposed registration metric is a good indicator of the degree of deformation.
CNN-based Lung CT Registration with Multiple Anatomical Constraints
Venue: arXiv cs.CV 2021
Year: 2021

Deep-learning-based registration methods emerged as a fast alternative to conventional registration methods. However, these methods often still cannot achieve the same performance as conventional registration methods because they are either limited to small deformation or they fail to handle a superposition of large and small deformations without producing implausible deformation fields with foldings inside. In this paper, we identify important strategies of conventional registration methods for lung registration and successfully developed the deep-learning counterpart. We employ a Gaussian-pyramid-based multilevel framework that can solve the image registration optimization in a coarse-to-fine fashion. Furthermore, we prevent foldings of the deformation field and restrict the determinant of the Jacobian to physiologically meaningful values by combining a volume change penalty with a curvature regularizer in the loss function. Keypoint correspondences are integrated to focus on the alignment of smaller structures. We perform an extensive evaluation to assess the accuracy, the robustness, the plausibility of the estimated deformation fields, and the transferability of our registration approach. We show that it achieves state-of-the-art results on the COPDGene dataset compared to conventional registration method with much shorter execution time. In our experiments on the DIRLab exhale to inhale lung registration, we demonstrate substantial improvements (TRE below $1.2$ mm) over other deep learning methods. Our algorithm is publicly available at https://grand-challenge.org/algorithms/deep-learning-based-ct-lung-registration/.
GitHub-OSS Fixit: Fixing bugs at scale in a Software Engineering Course
Venue: arXiv cs.SE 2021
Year: 2021

Many studies have shown the benefits of introducing open-source projects into teaching Software Engineering (SE) courses. However, there are several limitations of existing studies that limit the wide adaptation of open-source projects in a classroom setting, including (1) the selected project is limited to one particular project, (2) most studies only investigated on its effect on teaching a specific SE concept, and (3) students may make mistakes in their contribution which leads to poor quality code. Meanwhile, software companies have successfully launched programs like Google Summer of Code (GSoC) and FindBugs "fixit" to contribute to open-source projects. Inspired by the success of these programs, we propose GitHub-OSS Fixit, a course project where students are taught to contribute to open-source Java projects by fixing bugs reported in GitHub. We described our course outline to teach students SE concepts by encouraging the usages of several automated program analysis tools. We also included the carefully designed instructions that we gave to students for participating in GitHub-OSS Fixit. As all lectures and labs are conducted online, we think that our course design could help in guiding future online SE courses. Overall, our survey results show that students think that GitHub-OSS Fixit could help them to improve many skills and apply the knowledge taught in class. In total, 154 students have submitted 214 pull requests to 24 different Java projects, in which 59 of them have been merged, and 82 have been closed by developers.
LABNet: Local Graph Aggregation Network with Class Balanced Loss for Vehicle Re-Identification
Venue: arXiv cs.CV 2021
Year: 2021

Vehicle re-identification is an important computer vision task where the objective is to identify a specific vehicle among a set of vehicles seen at various viewpoints. Recent methods based on deep learning utilize a global average pooling layer after the backbone feature extractor, however, this ignores any spatial reasoning on the feature map. In this paper, we propose local graph aggregation on the backbone feature map, to learn associations of local information and hence improve feature learning as well as reduce the effects of partial occlusion and background clutter. Our local graph aggregation network considers spatial regions of the feature map as nodes and builds a local neighborhood graph that performs local feature aggregation before the global average pooling layer. We further utilize a batch normalization layer to improve the system effectiveness. Additionally, we introduce a class balanced loss to compensate for the imbalance in the sample distributions found in the most widely used vehicle re-identification datasets. Finally, we evaluate our method in three popular benchmarks and show that our approach outperforms many state-of-the-art methods.
Cyberphysical Security Through Resiliency: A Systems-centric Approach
Venue: arXiv cs.CR 2021
Year: 2021

Cyber-physical systems (CPS) are often defended in the same manner as information technology (IT) systems -- by using perimeter security. Multiple factors make such defenses insufficient for CPS. Resiliency shows potential in overcoming these shortfalls. Techniques for achieving resilience exist; however, methods and theory for evaluating resilience in CPS are lacking. We argue that such methods and theory should assist stakeholders in deciding where and how to apply design patterns for resilience. Such a problem potentially involves tradeoffs between different objectives and criteria, and such decisions need to be driven by traceable, defensible, repeatable engineering evidence. Multi-criteria resiliency problems require a system-oriented approach that evaluates systems in the presence of threats as well as potential design solutions once vulnerabilities have been identified. We present a systems-oriented view of cyber-physical security, termed Mission Aware, that is based on a holistic understanding of mission goals, system dynamics, and risk.
Soft-Robust Algorithms for Batch Reinforcement Learning
Venue: arXiv cs.LG 2021
Year: 2021

In reinforcement learning, robust policies for high-stakes decision-making problems with limited data are usually computed by optimizing the percentile criterion, which minimizes the probability of a catastrophic failure. Unfortunately, such policies are typically overly conservative as the percentile criterion is non-convex, difficult to optimize, and ignores the mean performance. To overcome these shortcomings, we study the soft-robust criterion, which uses risk measures to balance the mean and percentile criterion better. In this paper, we establish the soft-robust criterion's fundamental properties, show that it is NP-hard to optimize, and propose and analyze two algorithms to approximately optimize it. Our theoretical analyses and empirical evaluations demonstrate that our algorithms compute much less conservative solutions than the existing approximate methods for optimizing the percentile-criterion.
Optimizing the Neural Architecture of Reinforcement Learning Agents
Venue: arXiv cs.LG 2021
Year: 2021

Reinforcement learning (RL) enjoyed significant progress over the last years. One of the most important steps forward was the wide application of neural networks. However, architectures of these neural networks are typically constructed manually. In this work, we study recently proposed neural architecture search (NAS) methods for optimizing the architecture of RL agents. We carry out experiments on the Atari benchmark and conclude that modern NAS methods find architectures of RL agents outperforming a manually selected one.
Message Passing Based Structured Sparse Signal Recovery for Estimation of OTFS Channels with Fractional Doppler Shifts
Venue: arXiv cs.IT 2021
Year: 2021

The orthogonal time frequency space (OTFS) modulation has emerged as a promising modulation scheme for high mobility wireless communications. To enable efficient OTFS detection in the delay-Doppler (DD) domain, the DD domain channels need to be acquired accurately. To achieve the low latency requirement in future wireless communications, the time duration of the OTFS block should be small, therefore fractional Doppler shifts have to be considered to avoid significant modelling errors due to the assumption of integer Doppler shifts. However, there lack investigations on the estimation of OTFS channels with fractional Doppler shifts in the literature. In this work, we develop a high performing channel estimator for OTFS with the bi-orthogonal waveform or the rectangular waveform. Instead of estimating the DD domain channel directly, we estimate the channel gains and (fractional) Doppler shifts that parameterize the DD domain channel. The estimation is formulated as a structured signal recovery problem with a Bayesian treatment. Based on a factor graph representation of the problem, an efficient message passing algorithm is developed to recover the structured sparse signal (thereby the OTFS channel). The Cramer-Rao Lower Bound (CRLB) for the estimation is developed and the effectiveness of the algorithm is demonstrated through simulations.
Discovering Causal Structure with Reproducing-Kernel Hilbert Space $ε$-Machines
Venue: arXiv cs.LG 2021
Year: 2021

We merge computational mechanics' definition of causal states (predictively-equivalent histories) with reproducing-kernel Hilbert space (RKHS) representation inference. The result is a widely-applicable method that infers causal structure directly from observations of a system's behaviors whether they are over discrete or continuous events or time. A structural representation -- a finite- or infinite-state kernel $ε$-machine -- is extracted by a reduced-dimension transform that gives an efficient representation of causal states and their topology. In this way, the system dynamics are represented by a stochastic (ordinary or partial) differential equation that acts on causal states. We introduce an algorithm to estimate the associated evolution operator. Paralleling the Fokker-Plank equation, it efficiently evolves causal-state distributions and makes predictions in the original data space via an RKHS functional mapping. We demonstrate these techniques, together with their predictive abilities, on discrete-time, discrete-value infinite Markov-order processes generated by finite-state hidden Markov models with (i) finite or (ii) uncountably-infinite causal states and (iii) continuous-time, continuous-value processes generated by thermally-driven chaotic flows. The method robustly estimates causal structure in the presence of varying external and measurement noise levels and for very high dimensional data.
Doubly Stochastic Subspace Clustering
Venue: arXiv cs.LG 2021
Year: 2021

Many state-of-the-art subspace clustering methods follow a two-step process by first constructing an affinity matrix between data points and then applying spectral clustering to this affinity. Most of the research into these methods focuses on the first step of generating the affinity, which often exploits the self-expressive property of linear subspaces, with little consideration typically given to the spectral clustering step that produces the final clustering. Moreover, existing methods often obtain the final affinity that is used in the spectral clustering step by applying ad-hoc or arbitrarily chosen postprocessing steps to the affinity generated by a self-expressive clustering formulation, which can have a significant impact on the overall clustering performance. In this work, we unify these two steps by learning both a self-expressive representation of the data and an affinity matrix that is well-normalized for spectral clustering. In our proposed models, we constrain the affinity matrix to be doubly stochastic, which results in a principled method for affinity matrix normalization while also exploiting known benefits of doubly stochastic normalization in spectral clustering. We develop a general framework and derive two models: one that jointly learns the self-expressive representation along with the doubly stochastic affinity, and one that sequentially solves for one then the other. Furthermore, we leverage sparsity in the problem to develop a fast active-set method for the sequential solver that enables efficient computation on large datasets. Experiments show that our method achieves state-of-the-art subspace clustering performance on many common datasets in computer vision.
The $\aleph$ Calculus
Venue: arXiv cs.PL 2021
Year: 2021

Motivated by a need for a model of reversible computation appropriate for a Brownian molecular architecture, the $\aleph$ calculus is introduced. This novel model is declarative, concurrent, and term-based--encapsulating all information about the program data and state within a single structure in order to obviate the need for a von Neumann-style discrete computational 'machine', a challenge in a molecular environment. The name is inspired by the Greek for 'not forgotten', due to the emphasis on (reversibly) learning and un-learning knowledge of different variables. To demonstrate its utility for this purpose, as well as its elegance as a programming language, a number of examples are presented; two of these examples, addition/subtraction and squaring/square-rooting, are furnished with designs for abstract molecular implementations. A natural by-product of these examples and accompanying syntactic sugar is the design of a fully-fledged programming language, alethe, which is also presented along with an interpreter. Efficiently simulating $\aleph$ on a deterministic computer necessitates some static analysis of programs within the alethe interpreter in order to render the declarative programs sequential. Finally, work towards a type system appropriate for such a reversible, declarative model of computation is presented.
Vertex Sparsification for Edge Connectivity in Polynomial Time
Venue: arXiv cs.DS 2021
Year: 2021

An important open question in the area of vertex sparsification is whether $(1+ε)$-approximate cut-preserving vertex sparsifiers with size close to the number of terminals exist. The work Chalermsook et al. (SODA 2021) introduced a relaxation called connectivity-$c$ mimicking networks, which asks to construct a vertex sparsifier which preserves connectivity among $k$ terminals exactly up to the value of $c$, and showed applications to dynamic connectivity data structures and survivable network design. We show that connectivity-$c$ mimicking networks with $\widetilde{O}(kc^3)$ edges exist and can be constructed in polynomial time in $n$ and $c$, improving over the results of Chalermsook et al. (SODA 2021) for any $c \ge \log n$, whose runtimes depended exponentially on $c$.
Learning by Passing Tests, with Application to Neural Architecture Search
Venue: arXiv cs.LG 2021
Year: 2021

Learning through tests is a broadly used methodology in human learning and shows great effectiveness in improving learning outcome: a sequence of tests are made with increasing levels of difficulty; the learner takes these tests to identify his/her weak points in learning and continuously addresses these weak points to successfully pass these tests. We are interested in investigating whether this powerful learning technique can be borrowed from humans to improve the learning abilities of machines. We propose a novel learning approach called learning by passing tests (LPT). In our approach, a tester model creates increasingly more-difficult tests to evaluate a learner model. The learner tries to continuously improve its learning ability so that it can successfully pass however difficult tests created by the tester. We propose a multi-level optimization framework to formulate LPT, where the tester learns to create difficult and meaningful tests and the learner learns to pass these tests. We develop an efficient algorithm to solve the LPT problem. Our method is applied for neural architecture search and achieves significant improvement over state-of-the-art baselines on CIFAR-100, CIFAR-10, and ImageNet.
Multimodal Pretraining Unmasked: A Meta-Analysis and a Unified Framework of Vision-and-Language BERTs
Venue: arXiv cs.CL 2021
Year: 2021

Large-scale pretraining and task-specific fine-tuning is now the standard methodology for many tasks in computer vision and natural language processing. Recently, a multitude of methods have been proposed for pretraining vision and language BERTs to tackle challenges at the intersection of these two key areas of AI. These models can be categorised into either single-stream or dual-stream encoders. We study the differences between these two categories, and show how they can be unified under a single theoretical framework. We then conduct controlled experiments to discern the empirical differences between five V&L BERTs. Our experiments show that training data and hyperparameters are responsible for most of the differences between the reported results, but they also reveal that the embedding layer plays a crucial role in these massive models.
A Survey on Principles, Models and Methods for Learning from Irregularly Sampled Time Series
Venue: arXiv cs.LG 2021
Year: 2021

Irregularly sampled time series data arise naturally in many application domains including biology, ecology, climate science, astronomy, and health. Such data represent fundamental challenges to many classical models from machine learning and statistics due to the presence of non-uniform intervals between observations. However, there has been significant progress within the machine learning community over the last decade on developing specialized models and architectures for learning from irregularly sampled univariate and multivariate time series data. In this survey, we first describe several axes along which approaches to learning from irregularly sampled time series differ including what data representations they are based on, what modeling primitives they leverage to deal with the fundamental problem of irregular sampling, and what inference tasks they are designed to perform. We then survey the recent literature organized primarily along the axis of modeling primitives. We describe approaches based on temporal discretization, interpolation, recurrence, attention and structural invariance. We discuss similarities and differences between approaches and highlight primary strengths and weaknesses.
A Stitching Algorithm for Automated Surface Inspection of Rotationally Symmetric Components
Venue: arXiv cs.CV 2021
Year: 2021

This paper provides a novel approach to stitching surface images of rotationally symmetric parts. It presents a process pipeline that uses a feature-based stitching approach to create a distortion-free and true-to-life image from a video file. The developed process thus enables, for example, condition monitoring without having to view many individual images. For validation purposes, this will be demonstrated in the paper using the concrete example of a worn ball screw drive spindle. The developed algorithm aims at reproducing the functional principle of a line scan camera system, whereby the physical measuring systems are replaced by a feature-based approach. For evaluation of the stitching algorithms, metrics are used, some of which have only been developed in this work or have been supplemented by test procedures already in use. The applicability of the developed algorithm is not only limited to machine tool spindles. Instead, the developed method allows a general approach to the surface inspection of various rotationally symmetric components and can therefore be used in a variety of industrial applications. Deep-learning-based detection Algorithms can easily be implemented to generate a complete pipeline for failure detection and condition monitoring on rotationally symmetric parts.